Researchers have created a modular protein–foldamer pair that uses a large, well-defined binding interface to assemble hybrid nanostructures with controlled geometry.
Hybrid protein–molecule materials promise a way to combine biological structure with synthetic control, but the interface between the two has remained difficult to engineer. Existing approaches often rely on small binding pockets or flexible connectors, which can leave larger assemblies poorly positioned.
To address this, researchers at Ludwig-Maximilians-Universität München developed a protein–foldamer pair designed to act as a modular molecular connector. Foldamers are artificial molecules that, like proteins, can fold into stable shapes. Here, the team used a helical aromatic foldamer and searched for a protein partner able to recognize it selectively.
Using ribosome display, the researchers screened protein variants against the foldamer and identified C10, a variant of the Nanofitin scaffold. Biolayer interferometry showed that C10 bound the right-handed P-helix of the foldamer with nanomolar affinity, while no binding was detected for the left-handed M-helix.
“A specifically selected protein recognizes a synthetic molecule and binds to it with high affinity,” said study lead Ivan Huc in a recent press release. “The sizeable contact surface, which has a clearly defined structure, makes it possible to use the complex as a modular building block for larger molecular architectures.”
The team used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine how the two components fit together. The foldamer contacted a broad surface on the C10 scaffold through π-stacking, hydrophobic contacts, hydrogen bonding, and charge-reinforced hydrogen bonds. The structure showed a stable binding orientation that could be used for further architectural design.
Mass spectrometry was then used to assess larger assemblies formed from modified foldamer and protein components. Native nano-electrospray ionization mass spectrometry confirmed complexes in which one foldamer bound two C10 proteins, as well as assemblies in which foldamer duplexes bridged two proteins. Ion mobility measurements supported the expected differences in assembly size and shape.
By changing foldamer length and geometry, the researchers could vary the spacing and orientation of bound proteins. In crystal structures, the components formed cyclic assemblies and a one-dimensional zigzag network. Computational analysis indicated that the resulting lattice was porous, with the largest cavities able to accommodate spherical objects around five nanometers in diameter.
“Our results show that artificial foldamers can be used as precise connecting elements for protein architectures,” Huc said. “As it’s possible to change their length and chemical composition, they could in future play a role in helping to construct porous three-dimensional materials and introduce additional functional groups into such structures in the process.”
The immediate result is a proof-of-principle building block rather than a finished material. But the work shows how synthetic foldamers could give protein assemblies a level of geometric and chemical control that is difficult to achieve with flexible linkers or conventional small-molecule ligands.
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